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Title :   CRYSTAL STRUCTURE OF PUTATIVE HAD FAMILY HYDROLASE FROM STREPTOMYCES AVERMITILIS MA-4680

Authors :   V. N. Malashkevich, U. A. Ramagopal, R. Toro, J. M. Sauder, S. K. Burley, New York Sgx Research Center For Structural Genomics (Nysgx

Date :   20 Apr 10 (Deposition) - 28 Apr 10 (Release) - 28 Jan 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.84

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D  (2x)

Keywords :   Structural Genomics, Protein Structure Initiative, New York Structural Genomix Research Consortium, Nysgxrc, Hydrolase, Psi-2, New York Sgx Research Center For Structural Genomics (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. D. Daughtry, H. Huang, V. Malashkevich, Y. Patskovsky, W. Liu, U. Ramagopal, J. M. Sauder, S. K. Burley, S. C. Almo, D. Dunaway-Mariano, K. N. Allen
Structural Basis For The Divergence Of Substrate Specificit And Biological Function Within Had Phosphatases In Lipopolysaccharide And Sialic Acid Biosynthesis.
Biochemistry V. 52 5372 2013
PubMed-ID: 23848398 | Reference-DOI: 10.1021/BI400659K

Molecule 1 - PUTATIVE HAD FAMILY HYDROLASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	BC-PSGX3(BC)
	Expression System Strain	:	BL21(DE3)CODON+RIL
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	29829917, SAV3374, SAV_3374
	Organism Scientific	:	STREPTOMYCES AVERMITILIS
	Organism Taxid	:	227882
	Strain	:	MA-4680

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 14)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	CL	4	Ligand/Ion	CHLORIDE ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	MSE	8	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:18 , ASP A:20 , ASN A:110 , HOH A:187 , HOH A:200 , HOH A:224	BINDING SITE FOR RESIDUE CA A 500
02	AC2	SOFTWARE	GLY A:136 , ALA A:138 , HOH A:203 , GLY D:136 , ALA D:138 , HOH D:183 , HOH D:215	BINDING SITE FOR RESIDUE CA A 501
03	AC3	SOFTWARE	ARG A:42 , ARG A:72	BINDING SITE FOR RESIDUE CL A 503
04	AC4	SOFTWARE	ASP B:18 , ASP B:20 , ASN B:110 , HOH B:198 , HOH B:199 , HOH B:309	BINDING SITE FOR RESIDUE CA B 500
05	AC5	SOFTWARE	ARG B:72	BINDING SITE FOR RESIDUE CL B 503
06	AC6	SOFTWARE	ASP C:18 , ASP C:20 , ASN C:110 , HOH C:178 , HOH C:191 , HOH C:207	BINDING SITE FOR RESIDUE CA C 500
07	AC7	SOFTWARE	GLY B:136 , ALA B:138 , HOH B:180 , HOH B:181 , GLY C:136 , ALA C:138 , HOH C:195	BINDING SITE FOR RESIDUE CA B 501
08	AC8	SOFTWARE	ARG C:42 , GLY C:45 , ARG C:72	BINDING SITE FOR RESIDUE CL C 503
09	AC9	SOFTWARE	HOH B:217 , ASP D:18 , ASP D:20 , ASN D:110 , HOH D:191 , HOH D:437	BINDING SITE FOR RESIDUE CA D 500
10	BC1	SOFTWARE	ARG D:42 , ARG D:72	BINDING SITE FOR RESIDUE CL D 503

(no "SS Bond" information available for 3MMZ)

(no "Cis Peptide Bond" information available for 3MMZ)

(no "SAP(SNP)/Variant" information available for 3MMZ)

(no "PROSITE Motif" information available for 3MMZ)

(no "Exon" information available for 3MMZ)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:163
 aligned with Q82HY3_STRAW | Q82HY3 from UniProtKB/TrEMBL  Length:432

    Alignment length:163
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425   
         Q82HY3_STRAW   266 RPGALPTAEDIDAVVLDFDGTQTDDRVLIDSDGREFVSVHRGDGLGIAALRKSGLTMLILSTEQNPVVAARARKLKIPVLHGIDRKDLALKQWCEEQGIAPERVLYVGNDVNDLPCFALVGWPVAVASAHDVVRGAARAVTTVPGGDGAIREIASWILGPSLD 428
               SCOP domains d3mmza_ A: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.eeee...........ee.....eeeeeehhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhhhh.ee.......hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mmz A   2 SLGALPTAEDIDAVVLDFDGTQTDDRVLIDSDGREFVSVHRGDGLGIAALRKSGLTmLILSTEQNPVVAARARKLKIPVLHGIDRKDLALKQWCEEQGIAPERVLYVGNDVNDLPCFALVGWPVAVASAHDVVRGAARAVTTVPGGDGAIREIASWILGPSLD 164
                                    11        21        31        41        51      | 61        71        81        91       101       111       121       131       141       151       161   
                                                                                   58-MSE

Chain B from PDB  Type:PROTEIN  Length:163
 aligned with Q82HY3_STRAW | Q82HY3 from UniProtKB/TrEMBL  Length:432

    Alignment length:163
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425   
         Q82HY3_STRAW   266 RPGALPTAEDIDAVVLDFDGTQTDDRVLIDSDGREFVSVHRGDGLGIAALRKSGLTMLILSTEQNPVVAARARKLKIPVLHGIDRKDLALKQWCEEQGIAPERVLYVGNDVNDLPCFALVGWPVAVASAHDVVRGAARAVTTVPGGDGAIREIASWILGPSLD 428
               SCOP domains d3mmzb_ B: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh.eeee...........ee.....eeeeeehhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh..eee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhhhh.ee.......hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mmz B   2 SLGALPTAEDIDAVVLDFDGTQTDDRVLIDSDGREFVSVHRGDGLGIAALRKSGLTmLILSTEQNPVVAARARKLKIPVLHGIDRKDLALKQWCEEQGIAPERVLYVGNDVNDLPCFALVGWPVAVASAHDVVRGAARAVTTVPGGDGAIREIASWILGPSLD 164
                                    11        21        31        41        51      | 61        71        81        91       101       111       121       131       141       151       161   
                                                                                   58-MSE

Chain C from PDB  Type:PROTEIN  Length:162
 aligned with Q82HY3_STRAW | Q82HY3 from UniProtKB/TrEMBL  Length:432

    Alignment length:162
                                   276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426  
         Q82HY3_STRAW   267 PGALPTAEDIDAVVLDFDGTQTDDRVLIDSDGREFVSVHRGDGLGIAALRKSGLTMLILSTEQNPVVAARARKLKIPVLHGIDRKDLALKQWCEEQGIAPERVLYVGNDVNDLPCFALVGWPVAVASAHDVVRGAARAVTTVPGGDGAIREIASWILGPSLD 428
               SCOP domains d3mmzc_ C: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eeee.........eeee.....ee...hhhhhhhhhhhhhh..eeeee......hhhhhhhhhh..ee....hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhhhh.ee.......hhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mmz C   3 LGALPTAEDIDAVVLDFDGTQTDDRVLIDSDGREFVSVHRGDGLGIAALRKSGLTmLILSTEQNPVVAARARKLKIPVLHGIDRKDLALKQWCEEQGIAPERVLYVGNDVNDLPCFALVGWPVAVASAHDVVRGAARAVTTVPGGDGAIREIASWILGPSLD 164
                                    12        22        32        42        52     |  62        72        82        92       102       112       122       132       142       152       162  
                                                                                  58-MSE

Chain D from PDB  Type:PROTEIN  Length:174
 aligned with Q82HY3_STRAW | Q82HY3 from UniProtKB/TrEMBL  Length:432

    Alignment length:174
                                                                                                                                                                                                432       
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425      |  -    
         Q82HY3_STRAW   266 RPGALPTAEDIDAVVLDFDGTQTDDRVLIDSDGREFVSVHRGDGLGIAALRKSGLTMLILSTEQNPVVAARARKLKIPVLHGIDRKDLALKQWCEEQGIAPERVLYVGNDVNDLPCFALVGWPVAVASAHDVVRGAARAVTTVPGGDGAIREIASWILGPSLDSLDK-------   -
               SCOP domains d3mmzd_ D: automated matches                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -------------------------------------------------------------Hydrolase_3-3mmzD01 D:63-154                                                                --------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------Hydrolase_3-3mmzD02 D:63-154                                                                --------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------Hydrolase_3-3mmzD03 D:63-154                                                                --------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------Hydrolase_3-3mmzD04 D:63-154                                                                --------------------- Pfam domains (4)
         Sec.struct. author ............eeee.........eeeee....ee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhh..eee...hhhhhhhhhhhhhh.hhh.eeeee.hhhhhhhhhhh.eeee....hhhhhhhh.ee.......hhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3mmz D   2 SLGALPTAEDIDAVVLDFDGTQTDDRVLIDSDGREFVSVHRGDGLGIAALRKSGLTmLILSTEQNPVVAARARKLKIPVLHGIDRKDLALKQWCEEQGIAPERVLYVGNDVNDLPCFALVGWPVAVASAHDVVRGAARAVTTVPGGDGAIREIASWILGPSLDSLDKEGHHHHH 175
                                    11        21        31        41        51      | 61        71        81        91       101       111       121       131       141       151       161       171    
                                                                                   58-MSE

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: HAD-like (349)

Superfamily: HAD-like (349)

Family: automated matches (99)

Protein domain: automated matches (99)

Streptomyces avermitilis [TaxId: 227882] (1)

1a	d3mmza_	A:
1b	d3mmzb_	B:
1c	d3mmzc_	C:
1d	d3mmzd_	D:

(no "CATH Domain" information available for 3MMZ)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HAD (186)

Family: Hydrolase_3 (28)

Streptomyces avermitilis (1)

1a	Hydrolase_3-3mmzD01	D:63-154
1b	Hydrolase_3-3mmzD02	D:63-154
1c	Hydrolase_3-3mmzD03	D:63-154
1d	Hydrolase_3-3mmzD04	D:63-154

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q82HY3_STRAW | Q82HY3)

molecular function
	GO:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.
	GO:0016740		transferase activity		Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

Asymmetric Unit
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Biological Unit
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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